Fix: Support for chromosomes >1GB in size#36
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ad3002 wants to merge 2 commits intoBenson-Genomics-Lab:masterfrom
Open
Fix: Support for chromosomes >1GB in size#36ad3002 wants to merge 2 commits intoBenson-Genomics-Lab:masterfrom
ad3002 wants to merge 2 commits intoBenson-Genomics-Lab:masterfrom
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…nd consistency for amphibian chromosomes large than 1-2Gb
…uild and Apple Silicon support - Add build.sh: a dependency-free build script (uses CC env var, detects platform/arch, compiles src/trf.c) - Add Makefile.simple: minimal Makefile for building, versioned binary creation, install and test targets - Update README.md: document the simple build (build.sh), Makefile.simple usage, one-command gcc build, and native ARM Mac (Apple Silicon) support
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Problem
TRF crashed when processing T2T (telomere-to-telomere) chromosome assemblies longer than 1-2 GB. The errors varied depending on chromosome size, initially appearing to be a genome size issue but actually stemming from individual chromosome length limitations. Example Lissotriton helveticus genome assembly, chromosome: 4_1
The root cause was the use of 32-bit integer types (
int,unsigned int) for sequence indices and lengths, which limited processing to ~2GB (2^31 bytes for signed int).Solution
Replaced 32-bit integer types with 64-bit
size_ttypes throughout the codebase for all sequence-related indices, positions, and lengths. This enables TRF to process sequences up to system memory limits (theoretically 2^64 bytes).Changes by file
tr30dat.h - Core data type replacements:
int Length→size_t Length(global sequence length variable)unsigned int maxwraplength→size_t maxwraplengthFASTASEQUENCE,pairalign,TRFPARAMSET,bestperiodlistelement,distanceentry,distancelist,distanceseenarrayelement,distancelistelementtrfrun.h - Index and position variables:
index_liststructure (repeat positions)charcount,flankstart,flankendLoadSequenceFromFileBenson,LoadSequenceFromFileEugenetrf.c - Command-line parsing:
ParseSize()function usingstrtoull()for 64-bit values-lparameter parsing formaxwraplengthtr30dat.c - Memory allocation:
new1Darrayfuncmacro for correct memory allocation%d→%zufor all outputTesting
Successfully processes amphibian chromosomes and T2T assemblies exceeding 1-2 GB without crashes.